[2023-03-19 01:38:53,906] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:38:53,907] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:38:53,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg69533852-aeb1-49ce-aef8-8b05017bf31c/dqc_reference
[2023-03-19 01:38:54,987] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:38:54,987] [INFO] Task started: Prodigal
[2023-03-19 01:38:54,987] [INFO] Running command: cat /var/lib/cwl/stga78e8608-628a-4b9c-8679-a1af610c7695/OceanDNA-b21154.fa | prodigal -d OceanDNA-b21154/cds.fna -a OceanDNA-b21154/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:38:59,918] [INFO] Task succeeded: Prodigal
[2023-03-19 01:38:59,919] [INFO] Task started: HMMsearch
[2023-03-19 01:38:59,919] [INFO] Running command: hmmsearch --tblout OceanDNA-b21154/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69533852-aeb1-49ce-aef8-8b05017bf31c/dqc_reference/reference_markers.hmm OceanDNA-b21154/protein.faa > /dev/null
[2023-03-19 01:39:00,069] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:39:00,070] [INFO] Found 6/6 markers.
[2023-03-19 01:39:00,096] [INFO] Query marker FASTA was written to OceanDNA-b21154/markers.fasta
[2023-03-19 01:39:00,096] [INFO] Task started: Blastn
[2023-03-19 01:39:00,096] [INFO] Running command: blastn -query OceanDNA-b21154/markers.fasta -db /var/lib/cwl/stg69533852-aeb1-49ce-aef8-8b05017bf31c/dqc_reference/reference_markers.fasta -out OceanDNA-b21154/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:00,620] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:00,622] [INFO] Selected 19 target genomes.
[2023-03-19 01:39:00,623] [INFO] Target genome list was writen to OceanDNA-b21154/target_genomes.txt
[2023-03-19 01:39:00,635] [INFO] Task started: fastANI
[2023-03-19 01:39:00,635] [INFO] Running command: fastANI --query /var/lib/cwl/stga78e8608-628a-4b9c-8679-a1af610c7695/OceanDNA-b21154.fa --refList OceanDNA-b21154/target_genomes.txt --output OceanDNA-b21154/fastani_result.tsv --threads 1
[2023-03-19 01:39:11,592] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:11,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69533852-aeb1-49ce-aef8-8b05017bf31c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:39:11,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69533852-aeb1-49ce-aef8-8b05017bf31c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:39:11,592] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:39:11,592] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:39:11,592] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-19 01:39:11,593] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21154/tc_result.tsv
[2023-03-19 01:39:11,594] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:39:11,595] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:39:11,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69533852-aeb1-49ce-aef8-8b05017bf31c/dqc_reference/checkm_data
[2023-03-19 01:39:11,597] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:39:11,604] [INFO] Task started: CheckM
[2023-03-19 01:39:11,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21154/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21154/checkm_input OceanDNA-b21154/checkm_result
[2023-03-19 01:39:30,702] [INFO] Task succeeded: CheckM
[2023-03-19 01:39:30,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:39:30,728] [INFO] ===== Completeness check finished =====
[2023-03-19 01:39:30,728] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:39:30,728] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21154/markers.fasta)
[2023-03-19 01:39:30,728] [INFO] Task started: Blastn
[2023-03-19 01:39:30,728] [INFO] Running command: blastn -query OceanDNA-b21154/markers.fasta -db /var/lib/cwl/stg69533852-aeb1-49ce-aef8-8b05017bf31c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21154/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:39:31,557] [INFO] Task succeeded: Blastn
[2023-03-19 01:39:31,560] [INFO] Selected 12 target genomes.
[2023-03-19 01:39:31,561] [INFO] Target genome list was writen to OceanDNA-b21154/target_genomes_gtdb.txt
[2023-03-19 01:39:31,604] [INFO] Task started: fastANI
[2023-03-19 01:39:31,604] [INFO] Running command: fastANI --query /var/lib/cwl/stga78e8608-628a-4b9c-8679-a1af610c7695/OceanDNA-b21154.fa --refList OceanDNA-b21154/target_genomes_gtdb.txt --output OceanDNA-b21154/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:39:36,568] [INFO] Task succeeded: fastANI
[2023-03-19 01:39:36,575] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:39:36,575] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_905612265.1	s__LS-NOB sp905612265	96.5714	63	160	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014382285.1	s__LS-NOB sp014382285	83.6647	148	160	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.85	99.85	0.92	0.92	2	-
GCA_001542995.1	s__LS-NOB sp001542995	81.6996	136	160	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786505.1	s__LS-NOB sp002786505	80.387	118	160	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705185.1	s__LS-NOB sp002705185	79.84	97	160	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018653085.1	s__LS-NOB sp018653085	79.3537	123	160	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	-
GCA_003545625.1	s__LS-NOB sp003545625	78.8168	86	160	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	98.65	98.65	0.77	0.77	2	-
GCA_009873635.1	s__LS-NOB sp009873635	78.759	103	160	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.03	98.80	0.95	0.93	3	-
GCA_018673915.1	s__LS-NOB sp018673915	78.373	92	160	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.92	99.88	0.94	0.90	12	-
GCA_018664975.1	s__LS-NOB sp018664975	78.0222	72	160	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:39:36,576] [INFO] GTDB search result was written to OceanDNA-b21154/result_gtdb.tsv
[2023-03-19 01:39:36,579] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:39:36,581] [INFO] DFAST_QC result json was written to OceanDNA-b21154/dqc_result.json
[2023-03-19 01:39:36,581] [INFO] DFAST_QC completed!
[2023-03-19 01:39:36,581] [INFO] Total running time: 0h0m43s